Variant report

Variant	rs275754
Chromosome Location	chr15:40116727-40116728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40096907..40099731-chr15:40116417..40118536,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1027232	0.89[JPT][hapmap]
rs1836850	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35194933	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs275754	C15orf54	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40094400-40120400	Weak transcription	HSMMtube	muscle
2	chr15:40096200-40120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:40103000-40121400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:40110400-40129800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:40111600-40123400	Weak transcription	Aorta	Aorta
6	chr15:40112600-40120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:40112600-40121400	Weak transcription	Right Atrium	heart
8	chr15:40112800-40120000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:40112800-40120200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:40112800-40120400	Weak transcription	Osteobl	bone
11	chr15:40114200-40118000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:40114400-40120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:40114400-40121400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:40115600-40119200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:40115800-40120400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:40116000-40117000	ZNF genes & repeats	NHLF	lung
17	chr15:40116000-40122600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:40116200-40116800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:40116200-40117000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr15:40116200-40118000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:40116200-40122600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:40116400-40116800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr15:40116400-40117400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:40116600-40116800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:40116600-40117000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr15:40116600-40117000	Strong transcription	HSMM	muscle
27	chr15:40116600-40120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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